integrationPblkae: integrationPblkae

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

integrationPblkae

Description

This function execute integrationPblkae analysis which search for correspondence between clusters of two different experiments using clusters-pseudobulks generated using sparsely connected autoencoders. Thus, the function autoencoder4pseudoBulk has to be run in the two datasets before their comparison.

Usage

integrationPblkae(
  group = c("sudo", "docker"),
  scratch.folder,
  fileX = NULL,
  fileY = NULL,
  outputFolder,
  type = c("inter", "intra"),
  stats = c("anovalike", "pairwise")
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the path of the scratch folder
fileX	a character string indicating the path to the total.csv.for the 1st dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included.
fileY	a character string indicating the path to the total.csv.for the 2nd dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included.
outputFolder	where results are placed
type	two values inter, intra. Inter refers to comparison among clusters of two independent experiments. Intra comparisons among clusters of the same experiment
stats	two values anovalike, pairwise. Anovalike refers to comparison among clusters with respect to a pseudo reference sample. pairwise comparisons among all clusters by pairwise comparison

Value

a folder called psblkAE, which contains file called final_score.csv and all the intermediate files used to produce the integrated results.

Author(s)

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
 #inter
 library(rCASC)
 integrationPblkae(group="docker", 
        scratch.folder="/scratch", 
        fileX="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/setA1/permutation/total.csv",
        fileY="/data/clusters_association_paper/setA1_set1/set1/VandE/Results/set1/permutation/total.csv",
        outputFolder="/data/clusters_association_paper/setA1_set1",
        type="inter",
        stats="anovalike"
 )
 
 #intra
 library(rCASC)
 integrationPblkae(group="docker", 
        scratch.folder="/scratch", 
        fileX="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/setA1/permutation/total.csv",
        outputFolder="/data/clusters_association_paper/setA1_set1/setA1",
        type="intra",
        stats="pairwise"
 )

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.